3S37

Structural basis for the function of two anti-VEGF receptor antibodies

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies.

Franklin, M.C., Navarro, E.C., Wang, Y., Patel, S., Singh, P., Zhang, Y., Persaud, K., Bari, A., Griffith, H., Shen, L., Balderes, P., Kussie, P.

(2011) Structure 19: 1097-1107

  • DOI: https://doi.org/10.1016/j.str.2011.01.019
  • Primary Citation of Related Structures:  
    3S34, 3S35, 3S36, 3S37

  • PubMed Abstract: 

    • The anti-VEGF receptor 2 antibody IMC-1121B is a promising antiangiogenic drug being tested for treatment of breast and gastric cancer. We have determined the structure of the 1121B Fab fragment in complex with domain 3 of VEGFR2, as well as the structure of a different neutralizing anti-VEGFR2 antibody, 6 ...

    The anti-VEGF receptor 2 antibody IMC-1121B is a promising antiangiogenic drug being tested for treatment of breast and gastric cancer. We have determined the structure of the 1121B Fab fragment in complex with domain 3 of VEGFR2, as well as the structure of a different neutralizing anti-VEGFR2 antibody, 6.64, also in complex with VEGFR2 domain 3. The two Fab fragments bind at opposite ends of VEGFR2 domain 3; 1121B directly blocks VEGF binding, whereas 6.64 may prevent receptor dimerization by perturbing the domain 3:domain 4 interface. Mutagenesis reveals that residues essential for VEGF, 1121B, and 6.64 binding are nonoverlapping among the three contact patches.

    Organizational Affiliation: 

    Department of Immunology, ImClone Systems, New York, NY 10014, USA. mfranklin@nysbc.org



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1121B Fab light chainA [auth L]214Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1121B Fab heavy chainB [auth H]221Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2C [auth X]122Homo sapiensMutation(s): 0 
Gene Names: FLK1, KDR, VEGFR2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
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UniProt GroupP35968
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.284 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.684α = 90
b = 63.684β = 90
c = 275.028γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description, Source and taxonomy